6SJZ | pdb_00006sjz

HsNMT1 in complex with both MyrCoA and Acetylated-GNCFSKPR substrates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.202 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6SJZ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

High-resolution snapshots of human N-myristoyltransferase in action illuminate a mechanism promoting N-terminal Lys and Gly myristoylation.

Dian, C.Perez-Dorado, I.Riviere, F.Asensio, T.Legrand, P.Ritzefeld, M.Shen, M.Cota, E.Meinnel, T.Tate, E.W.Giglione, C.

(2020) Nat Commun 11: 1132-1132

  • DOI: https://doi.org/10.1038/s41467-020-14847-3
  • Primary Citation Related Structures: 
    6EHJ, 6QRM, 6SJZ, 6SK2, 6SK3, 6SK8, 6SKJ

  • PubMed Abstract: 

    The promising drug target N-myristoyltransferase (NMT) catalyses an essential protein modification thought to occur exclusively at N-terminal glycines (Gly). Here, we present high-resolution human NMT1 structures co-crystallised with reactive cognate lipid and peptide substrates, revealing high-resolution snapshots of the entire catalytic mechanism from the initial to final reaction states. Structural comparisons, together with biochemical analysis, provide unforeseen details about how NMT1 reaches a catalytically competent conformation in which the reactive groups are brought into close proximity to enable catalysis. We demonstrate that this mechanism further supports efficient and unprecedented myristoylation of an N-terminal lysine side chain, providing evidence that NMT acts both as N-terminal-lysine and glycine myristoyltransferase.


  • Organizational Affiliation
    • Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France.

Macromolecule Content 

  • Total Structure Weight: 97.2 kDa 
  • Atom Count: 7,209 
  • Modeled Residue Count: 797 
  • Deposited Residue Count: 822 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase 1
A, B
402Homo sapiensMutation(s): 0 
Gene Names: NMT1NMT
EC: 2.3.1.97 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens)
Explore P30419 
Go to UniProtKB:  P30419
PHAROS:  P30419
GTEx:  ENSG00000136448 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30419
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Apoptosis-inducing factor 3C [auth E],
D [auth F]
9Homo sapiensMutation(s): 2 
EC: 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96NN9 (Homo sapiens)
Explore Q96NN9 
Go to UniProtKB:  Q96NN9
PHAROS:  Q96NN9
GTEx:  ENSG00000183773 
Entity Groups
UniProt GroupQ96NN9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYA
(Subject of Investigation/LOI)

Query on MYA



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-QSGBVPJFSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.202 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.908α = 90
b = 178.9β = 90
c = 58.379γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-2010-BLAN-1611-01
French National Research AgencyFranceANR-10-LABX-0040-SPS
French National Research AgencyFranceFRISBI ANR-10-INSB-05-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary